Hi all, With respect to C. Groom,
"The sense I get from the small-molecule community is that they (we) have a great degree of well placed trust and see real value in pre-publication review of structures, not just papers - I'm sure this is true for the overwhelming majority of the macromolecular world too". Well, it is clear from this comment that in different fields there are different rules... . In macromolecular Xtallolgraphy, where some people deal with biologists from biomedical sciences, the impact of journals is an important aspect during evaluation and, unfortunately, pre-publication review of structures has no actual value in their field. For a structural BIO-logist in biomedical sciences, a paper it is not "just a paper", it is an effort of years reduced to a (or few) paper(s). The non-structural BIO-people understand what is a Cell paper, but not at all about what it is a pre-publication of a structure. My thougts go in the direction of grant applications, fellowships, promotion, all filtered by the impact factor but not by pre-publication of structures which, btw, it is neither considered in the h-index of a researcher. To find a good solution is difficult. The easiest way is to ask for coordinates and maps... which is truly uncomfortable considering the possibility of a reviewer solving its own structure by molecular replacement. If it is possible to generate false data, it is much more easy to "invent" the way the structure was solved without telling which "PDB code" (=reviewed coordinates) was used. This, together with the trick of saying that the structure is not good enough, please improve the data quality and, in the meantime, I publish my own one (this time yes, it's solved by reviewer's means), is not clear to me. I feel very sorry in being so paranoid! I understand the will of proper revision. But do "gel"-biologists, also with good criteria of quality, ask for samples shown in a figure of a gel ? Best, Maria PD. With all this I do not want to say that the reviewer of Marc Kvansakul's structure is going to do all this type of things, I am sure it's a good reviewer with the strict intention to do a proper job. On 19 April 2012 15:55, George M. Sheldrick <gshe...@shelx.uni-ac.gwdg.de>wrote: > Colin, > > Speaking as someone who has one foot in small molecule crystallography > and the other in macromolecular, I have to say that attitudes are > completely different, and that there are good reasons for this. A PhD > student or junior postdoc in a macromolecular lab may have spent the > last three (or more) years cloning, expressing. purifying and > crystallizing a protein, and it is very likely that three or more groups > elsewhere in the world are working on the same target. Even if the > organisms are different, usually only one group will be able to publish > in a high-profile journal, so being scooped is a major worry and happens > frequently, even when all concerned are completely honest. A single > small molecule structure is a very much smaller part of the average > chemical PhD which often involves dozens of structures, and a couple of > duplicated structures will have little influence on the future career of > the PhD student. > > Releasing the PDB hold on a structure just before submitting the paper > has something to be said for it. I would like to do this more often, but > it is usually vetoed by paranoid biological co-authors. Even if one is > providing the competition with a good MR model, at least they will have > to cite it. > > George > > On 04/19/2012 03:09 PM, Colin Groom wrote: > > It has always struck me as something of a surprise that pre-publication > review of structures in protein-land > differs so significantly from small molecule-land. One of the activities > of the CCDC is to supply pre-release > CSD structures to referees, using a simple, automated system to > establish that the requestors are referees. > This avoids the need for any involvement of the depositor or journal and > allows a centralised record to be kept > as to who saw which structures and when (although, to my knowledge, we > have never needed to refer to this). > In 2012, requests have averaged at about 5 a day, but the real figure > is probably much higher, as some journals > provide this facility themselves. The sense I get from the > small-molecule community is that they (we) have a > great degree of well placed trust and see real value in pre-publication > review of structures, not just papers - > I'm sure this is true for the overwhelming majority of the > macromolecular world too. > > > > Colin > > > > -----Original Message----- > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > herman.schreu...@sanofi.com > > Sent: 19 April 2012 13:54 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers > > > > This is off course a valid point. A desperate graduate student faking a > > structure risks his or hers career and reputation, while an anonymous > > referee, "borrowing" someone else's results gets away without any risk > > of being caught. Besides making the name of the reviewer public, I see > > other options: > > > > 1) submit the coordinates and structure factors to the pdb to get a > > priority date as has been suggested before. Many journals require > > anyways a pdb code before acceptance of the paper. One could even > > publish this priority date in the paper in the footnote where the pdb > > code is mentioned. > > 2) require from referees a conflict-of-interest-statement that they, or > > close colleagues are not working on the same or a very similar > > structure. If an author gets the impression that he may have been > > scooped by a less-ethical referee, he could ask the journal to verify > > that the referees of his rejected paper were not involved in the > > accelerated publication. If it turns out that a referee has made a false > > statement this would clearly constitute fraud and a reason for > > repercussions. > > > > Herman > > > > > > -----Original Message----- > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > > Jobichen Chacko > > Sent: Thursday, April 19, 2012 2:12 PM > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers > > > > Dear All, > > Here comes the problem of blind reveiw, the authors are always at the > > receving end to share all there data, results and now the full > > cordinates to an unknown person, just trusting the journal editor. Why > > don't the journals think about making the name of the reviewer also > > public. > > > > Eventhough the persons advocated giving the cordinates, there were cases > > of holding the paper for reveiw for few months and finally rejecting it, > > while a very close article appeared as accelerated publn within few > > weeks of rejection of the original paper. Refer to the previous > > discussion on fake structure. > > > > Again it depends on how close you are towards the acceptance. Also > > hesitation to give away your cordiantes without any guarantee of > > publishing it in that journal cannot be considered as a big sin, > > especially if someone's graduation is depend on a single paper. > > > > Jobi > > > > > > > > On Thu, Apr 19, 2012 at 6:34 AM, Marc Kvansakul > > <m.kvansa...@latrobe.edu.au> wrote: > >> Dear CCP4BBlers, > >> > >> I was wondering how common it is that reviewers request to have a copy > > > >> of the PDB coordinate file for the review purpose. I have just been > >> asked to supply this by an editor after several weeks of review, after > > > >> one of the reviewers requested a copy. > >> > >> Not having ever been asked to do this before I feel just a tad > >> uncomfortable about handing this over... > >> > >> Your opinions would be greatly appreciated. > >> > >> Best wishes > >> > >> Marc > >> > >> Dr. Marc Kvansakul > >> Laboratory Head, NHMRC CDA Fellow > >> Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci > > > >> Bld 4, Kingsbury Drive, Melbourne, 3086, Australia > >> T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.au | > >> > > > > LEGAL NOTICE > > Unless expressly stated otherwise, information contained in this > > message is confidential. If this message is not intended for you, > > please inform postmas...@ccdc.cam.ac.uk and delete the message. > > The Cambridge Crystallographic Data Centre is a company Limited > > by Guarantee and a Registered Charity. > > Registered in England No. 2155347 Registered Charity No. 800579 > > Registered office 12 Union Road, Cambridge CB2 1EZ. > > > > -- > Prof. George M. Sheldrick FRS > Dept. Structural Chemistry, > University of Goettingen, > Tammannstr. 4, > D37077 Goettingen, Germany > Tel. +49-551-39-3021 or -3068 > Fax. +49-551-39-22582 > -- Maria Solà Dep. Structural Biology IBMB-CSIC Baldiri Reixach 10-12 08028 BARCELONA Spain Tel: (+34) 93 403 4950 Fax: (+34) 93 403 4979 e-mail: maria.s...@ibmb.csic.es
